# Patient Trajectory Prediction: Integrating Clinical Notes with Transformers

arXiv: https://arxiv.org/abs/2502.18009 · HTML: https://mlsanity.com/paper/2502.18009/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 25 references that are in the map.
- First posted on arXiv 25 Feb 2025.

## Builds on (most cited first, 13 of 13)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [RETAIN: An Interpretable Predictive Model for Healthcare using Reverse Time Attention Mechanism](https://mlsanity.com/paper/1608.05745/) (2016)
- [Doctor AI: Predicting Clinical Events via Recurrent Neural Networks](https://mlsanity.com/paper/1511.05942/) (2015)
- [Lessons from Natural Language Inference in the Clinical Domain](https://mlsanity.com/paper/1808.06752/) (2018)
- [Why Exposure Bias Matters: An Imitation Learning Perspective of Error Accumulation in Language Generation](https://mlsanity.com/paper/2204.01171/) (2022)
- [Beyond the Limits: A Survey of Techniques to Extend the Context Length in Large Language Models](https://mlsanity.com/paper/2402.02244/) (2024)
- [Automated Medical Coding on MIMIC-III and MIMIC-IV: A Critical Review and Replicability Study](https://mlsanity.com/paper/2304.10909/) (2023)
- [MosaicBERT: A Bidirectional Encoder Optimized for Fast Pretraining](https://mlsanity.com/paper/2312.17482/) (2023)
- [A Survey on Training Challenges in Generative Adversarial Networks for Biomedical Image Analysis](https://mlsanity.com/paper/2201.07646/) (2022)
- [Hawkes Processes Modeling, Inference and Control: An Overview](https://mlsanity.com/paper/2011.13073/) (2020)

## Abstract (arXiv)

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.